Abstract
This study is to investigate the genome sequence of Serratia sp. S2. The genomic DNA of Serratia sp. S2 was extracted and the sequencing library was constructed. The sequencing was carried out by Illumina 2000 and complete genomic sequences were obtained. Gene function annotation and bioinformatics analysis were performed by comparing with the known databases. The genome size of Serratia sp. S2 was 5,604,115 bp and the G+C content was 57.61%. There were 5373 protein coding genes, and 3732, 3614, and 3942 genes were respectively annotated into the GO, KEGG, and COG databases. There were 12 genes related to chromium metabolism in the Serratia sp. S2 genome. The whole genome sequence of Serratia sp. S2 is submitted to the GenBank database with gene accession number of LNRP00000000. Our findings may provide theoretical basis for the subsequent development of new biotechnology to repair environmental chromium pollution.
Similar content being viewed by others
References
Dadrasnia, A., Chuan Wei, K. S., Shahsavari, N., Azirun, M. S., & Ismail, S. (2015). Biosorption potential of Bacillus salmalaya strain 139SI for removal of Cr(VI) from aqueous solution. International Journal of Environmental Research and Public Health, 12, 15321–15338.
Khatoon, N., Husain Khan, A., Pathak, V., Agnihotri, N., & Rehman, M. (2013). Removal of hexavalent chromium from synthetic wastewater using synthetic Nano Zerovalent iron (NZVI) as adsorbent. International Journal of Innovative Research in Science, Engineering and Technology, 11, 6140–6149.
Malaviya, P., & Singh, A. (2016). Bioremediation of chromium solutions and chromium containing wastewaters. Critical Reviews in Microbiology, 42, 607–633.
Liu, X., Wu, G., Zhang, Y., Wu, D., Li, X., & Liu, P. (2015). Chromate reductase YieF from Escherichia coli enhances hexavalent chromium resistance of human HepG2 cells. International Journal of Molecular Sciences, 16, 11892–11902.
Dey, S., & Paul, A. K. (2016). Evaluation of chromate reductase activity in the cell-free culture filtrate of Arthrobacter sp. SUK 1201 isolated from chromite mine overburden. Chemosphere, 156, 69–75.
Sarkar, A., Sar, P., & Islam, E. (2016). Hexavalent chromium reduction by microbacterium oleivorans A1: a possible mechanism of chromate -detoxification and -bioremediation. Recent Patents on Biotechnology, 9, 116–129.
Bhattacharya, P., Barnebey, A., & Zemla, M. (2015). Complete genome sequence of the chromate-reducing bacterium Thermoanaerobacter thermohydrosulfuricus strain BSB-33. Standards in Genomic Sciences, 5, 74.
Mabrouk, M. E., Arayes, M. A., & Sabry, S. A. (2014). Hexavalent chromium reduction by chromate-resistant haloalkaliphilic Halomonas sp. M-Cr newly isolated from tannery effluent. Biotechnology and Biotechnological Equipment, 28, 659–667.
Ge, S., Ai, W., & Dong, X. (2016). High-quality draft genome sequence of Leucobacter sp. strain G161, a distinct and effective chromium reducer. Genome Announcements, 4, e01760–e01715.
Bonnin, R. A., Girlich, D., Imanci, D., Dortet, L., & Naas, T. (2015). Draft genome sequence of the Serratia rubidaea CIP 103234T reference strain, a human-opportunistic pathogen. Genome Announcements, 3, 2169–8287.
Lian, J., Li, Z., Xu, Z., Guo, J., Hu, Z., Guo, Y., Li, M., & Yang, J. (2016). Isolation and Cr(VI) reduction characteristics of quinone respiration in mangrovibacter plantisponsor strain cr1. Biotechnology and Applied Biochemistry, 63, 595–600.
Deng, P., Tan, X., Wu, Y., Bai, Q., Jia, Y., & Xiao, H. (2013). Cloning and sequence analysis of FMN red gene fragment from Serratia sp. CQMUS2. Biotechnology, 23, 8–11.
He, Y., Dong, L., Zhou, S., Jia, Y., Bai, Q.,Wang, R., Xiao, H. (2013). Screening of Hexavalent chromiumresistant Serratia sp. S2 and the reduction characeristics of Cr(VI). Modern Preventive Medicine, 18, 3374–3378.
O'Brien, C. L., Pavli, P., Gordon, D. M., & Allison, G. E. (2014). Detection of bacterial DNA in lymph nodes of Crohn’s disease patients using high throughput sequencing. Gut, 63, 1596–1606.
Echeverría-Vega, A., Morales-Vicencio, P., Saez-Saavedra, C., Ceh, J., & Araya, R. (2016). The complete genome sequence and analysis of vB_VorS-PVo5, a Vibrio phage infectious to the pathogenic bacterium Vibrio ordalii ATCC-33509. Standards in Genomic Sciences, 11, 45.
Zhang, G., Wang, J., Yang, J., Li, W., Deng, Y., Li, J., Huang, J., Hu, S. and Zhang, B. (2015). Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics, 581–590.
Peng, Y., Lai, Z., Lane, T., Nageswara-Rao, M., Okada, M., Jasieniuk, M., O’Geen, H., Kim, R. W., Sammons, R. D., Rieseberg, L. H., & Stewart Jr., C. N. (2014). De novo genome assembly of the economically important weed horseweed using integrated data from multiple sequencing platforms. Plant Physiology, 166, 1241–1254.
Benson, G. (1999). Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27, 573–580.
Lagesen, K., Hallin, P., Rødland, E. A., Staerfeldt, H. H., Rognes, T., & Ussery, D. W. (2007). RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research, 35, 3100–3108.
Lowe, T. M., & Eddy, S. R. (1997). tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research, 25, 955–964.
Gardner, P. P., Daub, J., Tate, J. G., Nawrocki, E. P., Kolbe, D. L., Lindgreen, S., Wilkinson, A. C., Finn, R. D., Griffiths-Jones, S., Eddy, S. R. and Bateman, A. (2009). Rfam: updates to the RNA families database. Nucleic Acids Research, D136–140.
Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., & Hattori, M. (2004). The KEGG resource for deciphering the genome. Nucleic Acids Research, 32, D277–D280.
Kanehisa, M. (1997). A database for post-genome analysis. Trends in Genetics, 13, 375–376.
Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., & Hirakawa, M. (2006). From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Research, 34, D354–D357.
Bard, J. and Winter, R. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25–29.
Tatusov, R. L., Koonin, E. V., & Lipman, D. J. (1997). A genomic perspective on protein families. Science, 278, 631–637.
Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y. I., Yin, J. J., & Natale, D. A. (2003). The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 11, 41.
Diaz-Perez, C., Cervantes, C., Campos-Garcia, J., Julian-Sanchez, A., & Riveros-Rosas, H. (2007). Phylogenetic analysis of the chromate ion transporter (CHR) superfamily. The FEBS Journal, 6215–6227.
Ackerley, D. F., Gonzalez, C. F., Park, C. H., Blake II, R., Keyhan, M., & Matin, A. (2004). Chromate-reducing properties of soluble flavoproteins from Pseudomonas putida and Escherichia coli. Applied and Environmental Microbiology, 70, 873–882.
Juhnke, S., Peitzsch, N., Hübener, N., Grosse, C. and Nies, D. H. (2002). New genes involved in chromate resistance in Ralstonia metallidurans strain CH34. Archives of Microbiology, 15–25.
Coelho, C., Branco, R., Natal-da-Luz, T., Sousa, J. P., & Morais, P. V. (2015). Evaluation of bacterial biosensors to determine chromate bioavailability and to assess ecotoxicity of soils. Chemosphere, 62–69.
Branco, R., Chung, A. P., Johnston, T., Gurel, V., Morais, P., & Zhitkovich, A. (2008). The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide. Journal of Bacteriology, 190, 6996–7003.
Chihomvu, P., Stegmann, P., & Pillay, M. (2015). Characterization and structure prediction of partial length protein sequences of pcoA, pcoR and chrB genes from heavy metal resistant bacteria from the Klip River, South Africa. International Journal of Molecular Sciences, 16, 7352–7374.
Aguilar-Barajas, E., Paluscio, E., Cervantes, C. and Rensing, C. (2008). Expression of chromate resistance genes from Shewanella sp. strain ANA-3 in Escherichia coli. FEMS Microbiology Letters, 97–100.
Beller, H. R., Han, R., Karaoz, U., Lim, H., & Brodie, E. L. (2013). Genomic and physiological characterization of the chromate-reducing, aquifer-derived Firmicute Pelosinus sp. strain HCF1. Applied and Environmental Microbiology, 79, 63–73.
Sarangi, A., & Krishnan, C. (2016). Detoxification of hexavalent chromium by Leucobacter sp. uses a reductase with specificity for dihydrolipoamide. Journal of Basic Microbiology, 56, 175–183.
Mugerfeld, I., Law, B. A., Wickham, G. S., & Thompson, D. K. (2009). A putative azoreductase gene is involved in the Shewanella oneidensis response to heavy metal stress. Applied Microbiology and Biotechnology, 82, 1131–1141.
Maqbool, Z., Hussain, S., Ahmad, T., Nadeem, H., Imran, M., Khalid, A., Abid, M., & Martin-Laurent, F. (2016). Use of RSM modeling for optimizing decolorization of simulated textile wastewater by Pseudomonas aeruginosa strain ZM130 capable of simultaneous removal of reactive dyes and hexavalent chromium. Environmental Science and Pollution Research International, 23, 11224–11239.
Joutey, N. T., Sayel, H., Bahafid, W., & El Ghachtouli, N. (2015). Mechanisms of hexavalent chromium resistance and removal by microorganisms. Reviews of Environmental Contamination and Toxicology, 233, 45–69.
Chaudhari, A. U., Tapase, S. R., Markad, V. L., & Kodam, K. M. (2013). Simultaneous decolorization of reactive Orange M2R dye and reduction of chromate by Lysinibacillus sp. KMK-A. Journal of Hazardous Materials, 262, 580–588.
Morais, P. V., Branco, R., & Francisco, R. (2011). Chromium resistance strategies and toxicity: what makes Ochrobactrum tritici 5bvl1 a strain highly resistant. Biometals, 401–410.
Wakatsuki, T. (1995). Metal oxidoreduction by microbial cells. Journal of Industrial Microbiology, 14, 169–177.
Puzon, G. J., Petersen, J. N., Roberts, A. G., Kramer, D. M., & Xun, L. (2002). A bacterial flavin reductase system reduces chromate to a soluble chromium (III)-NAD(+) complex. Biochemical and Biophysical Research Communications, 294, 76–81.
Otwell, A. E., Sherwood, R. W., Zhang, S., Nelson, O. D., Li, Z., Lin, H., Callister, S. J., & Richardson, R. E. (2015). Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay. Environmental Microbiology, 17, 1977–1990.
Willetts, A., & Kelly, D. R. (2014). Multiple native flavin reductases in camphor-metabolizing Pseudomonas putida NCIMB 10007: functional interaction with two-component diketocamphane monooxygenase isoenzymes. Microbiology, 160, 1783–1794.
Xue, X. M., Yan, Y., Xu, H. J., Wang, N., Zhang, X., & Ye, J. (2014). ArsH from Synechocystis sp. PCC 6803 reduces chromate and ferric iron. FEMS Microbiology Letters, 356, 105–120.
Sedláček, V., & Kučera, I. (2010). Chromate reductase activity of the Paracoccus denitrificans ferric reductase B (FerB) protein and its physiological relevance. Archives of Microbiology, 192, 919–926.
He, M., Li, X., Guo, L., Miller, S. J., Rensing, C., & Wang, G. (2010). Characterization and genomic analysis of chromate resistant and reducing Bacillus cereus strain SJ1. BMC Microbiology, 10, 221–227.
He, M., Li, X., Liu, H., Miller, S. J., Wang, G., & Rensing, C. (2011). Characterization and genomic analysis of a highly chromate resistant and reducing bacterial strain Lysinibacillus fusiformis ZC1. Journal of Hazardous Materials, 185, 682–688.
Funding
This work was supported by the National Natural Science Foundation of China [grant number 21403021], the Scientific and Technological Research projects of Chongqing city Board of Education [grant number KJ1500216], and the Students Scientific Research and Innovation Project of Chongqing Medical University [grant number. 201722].
Author information
Authors and Affiliations
Contributions
Hong Xiao contributes to conception and design of experiments. Lanlan Dong and Simin Zhou carried out experiments. Yuan He and Peng Deng performed analysis and interpretation of data. Lanlan Dong and Simin Zhou contribute to the writing and redrafting of the manuscript. Jieying Gao and Yan Jia revise the manuscript critically for important intellectual content. Qunhua Bai approves the final version to be published. All authors read and approve the final manuscript.
Corresponding author
Ethics declarations
Conflict of Interest
All authors declare no financial competing interests.
All authors declare no non-financial competing interests.
Rights and permissions
About this article
Cite this article
Dong, L., Zhou, S., He, Y. et al. Analysis of the Genome and Chromium Metabolism-Related Genes of Serratia sp. S2. Appl Biochem Biotechnol 185, 140–152 (2018). https://doi.org/10.1007/s12010-017-2639-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12010-017-2639-5